Get the path to the files generated by the pipeline for the samples of all sequencings and projects.
Parameters
Name
Type
Description
Default
cfg
dict
Dict representing the configuration of an analysis with the chromake pipeline.
required
mode
str
String representing the files to get. Accepted values are: - sequencing (raw fastq) - multiqc_raw (multiqc report regrouping the fastqc of the raw fastq files) - cutadapt (fastq after adapter trimming) - fastqc_trimmed (fastqc reports after the adapter trimming) - multiqc_trimmed (multiqc report after adapter trimming) - bam (bam files after alignment with bowtie2) - bam_filtered_coord (bam files after filtering the non-standard chromosomes and sorted by coordinate) - bam_filtered_name (bam files after filtering the non-standard chromosomes and sorted by name) - bedgraph (bedGrapg files generated by HOMER for UCSC visualisation)
Get the files necessary for the macs2/macs3 rules of a project.
Parameters
Name
Type
Description
Default
cfg
dict
Dict representing the configuration of an analysis with the chromake pipeline.
required
project_name
str
String representing the name of the project in cfg
required
mode
str
String indicating the output. Accepted values are: - macs (dict with all inputs and the outputs of the macs3 command for all samples associated with the project) - macs_output (list of all outputs of the macs3 command for the project)
Get the path to the files generated by the pipeline for the samples of a specific sequencing.
Parameters
Name
Type
Description
Default
cfg
dict
Dict representing the configuration of an analysis with the chromake pipeline.
required
sequencing_name
str
String representing the name of the sequencing
required
mode
str
String representing the files to get. Accepted values are: - sequencing (raw fastq) - multiqc_raw (multiqc report regrouping the fastqc of the raw fastq files) - cutadapt (fastq after adapter trimming) - fastqc_trimmed (fastqc reports after the adapter trimming) - multiqc_trimmed (multiqc report after adapter trimming) - bam (bam files after alignment with bowtie2) - bam_filtered (bam files after filtering the non-standard chromosomes) - flagstat (output of samtools flagstat on the bam files) - stats (output of samtools stats on the bam files) - multiqc_stats (multiqc on the folder containing the stats output)